Changed it to use a tooltip. God I hate CSS.

locales/en/messages.json

@@ -2301,13 +2301,15 @@
     "dataflashFirmwareUpgradeRequired": {
         "message": "Dataflash requires firmware >= 1.8.0."
     },
-    "dataflashSavingDeprecationNote": {
-        "message": "(Deprecated, use '<b>$t(onboardLoggingRebootMscText.message)</b>' below:",
-        "description": "Used to indicate that saving log files through configurator is deprecated if MSC is available. Note: The seemingly unbalanced opening brace is intentional, there is a closing brace in a separate DOM element after the button."
-    },
     "dataflashButtonSaveFile": {
         "message": "Save flash to file..."
     },
+    "dataflashButtonSaveFileDeprecated": {
+        "message": "Save flash to file... (deprecated)"
+    },
+    "dataflashSaveFileDepreciationHint": {
+        "message": "Saving blackbox logs through the configurator is slow and relatively prone to errors. It is recommended that you instead use '<b>$t(onboardLoggingRebootMscText.message)</b>' (below) to activate the Mass Storage Mode, and access your flight controller as a storage device to download the log files."
+    },
     "dataflashButtonErase": {
         "message": "Erase flash"
     },

src/css/tabs/onboard_logging.css

@@ -1,3 +1,41 @@
+.tab-onboard_logging .regular-button {
+    margin-top: 8px;
+    margin-bottom: 8px;
+    margin-right: 10px;
+    background-color: #ffbb00;
+    border-radius: 3px;
+    border: 1px solid #dba718;
+    color: #000;
+    font-family: 'open_sansbold', Arial;
+    font-size: 12px;
+    text-shadow: 0px 1px rgba(255, 255, 255, 0.25);
+    display: inline-block;
+    cursor: pointer;
+    transition: all ease 0.2s;
+    padding: 0px;
+    padding-left: 9px;
+    padding-right: 9px;
+    line-height: 28px;
+}
+.tab-onboard_logging .regular-button:hover {
+    background-color: #ffcc3e;
+    transition: all ease 0.2s;
+}
+.tab-onboard_logging .regular-button:active {
+    background-color: #ffcc3e;
+    transition: all ease 0.0s;
+    box-shadow: inset 0px 1px 5px rgba(0, 0, 0, 0.35);
+}
+.tab-onboard_logging .regular-button.disabled {
+    cursor: default;
+    color: #fff;
+    background-color: #AFAFAF;
+    border: 1px solid #AFAFAF;
+    pointer-events: none;
+    text-shadow: none;
+    opacity: 0.5;
+}
+
 .tab-onboard_logging .info {
     margin: 0 0 10px 0;
     position: relative;
@@ -145,6 +183,19 @@
     border-radius: 5px;
 }
 
+.dataflash-buttons {
+    display: inline-block;
+}
+
+.tab-onboard_logging .save-flash .helpicon {
+    margin-left: 7px;
+    margin-right: 0px;
+    margin-top: 4px;
+    margin-bottom: 0px;
+    display: inline-block;
+    float: unset;
+}
+
 .dataflash-confirm-erase.erasing .dataflash-erase-progress {
     display: block;
 }
@@ -206,12 +257,20 @@
     display: none;
 }
 
-.require-msc-supported {
+.tab-onboard_logging .require-msc-supported {
     display: none;
 }
 
 .tab-onboard_logging.msc-supported .require-msc-supported {
-    display: unset;
+    display: inherit;
+}
+
+.tab-onboard_logging .require-msc-not-supported {
+    display: inherit;
+}
+
+.tab-onboard_logging.msc-supported .require-msc-not-supported {
+    display: none;
 }
 
 .require-msc-not-ready {
@@ -279,41 +338,3 @@
     
     border-radius: 45px;
 }
-
-.tab-onboard_logging .regular-button {
-    margin-top: 8px;
-    margin-bottom: 8px;
-    margin-right: 10px;
-    background-color: #ffbb00;
-    border-radius: 3px;
-    border: 1px solid #dba718;
-    color: #000;
-    font-family: 'open_sansbold', Arial;
-    font-size: 12px;
-    text-shadow: 0px 1px rgba(255, 255, 255, 0.25);
-    display: inline-block;
-    cursor: pointer;
-    transition: all ease 0.2s;
-    padding: 0px;
-    padding-left: 9px;
-    padding-right: 9px;
-    line-height: 28px;
-}
-.tab-onboard_logging .regular-button:hover {
-    background-color: #ffcc3e;
-    transition: all ease 0.2s;
-}
-.tab-onboard_logging .regular-button:active {
-    background-color: #ffcc3e;
-    transition: all ease 0.0s;
-    box-shadow: inset 0px 1px 5px rgba(0, 0, 0, 0.35);
-}
-.tab-onboard_logging .regular-button.disabled {
-    cursor: default;
-    color: #fff;
-    background-color: #AFAFAF;
-    border: 1px solid #AFAFAF;
-    pointer-events: none;
-    text-shadow: none;
-    opacity: 0.5;
-}

src/js/msp/MSPHelper.js

@@ -1271,7 +1271,9 @@ MspHelper.prototype.process_data = function(dataHandler) {
 
             switch (code) {
             case MSPCodes.MSP_SET_REBOOT:
-                showErrorDialog(i18n.getMessage('operationNotSupported'));
+                TABS.onboard_logging.mscRebootFailedCallback();
+
+                break;
             }
         }
     }

src/js/tabs/onboard_logging.js

@@ -582,3 +582,10 @@ TABS.onboard_logging.cleanup = function (callback) {
         callback();
     }
 };
+
+TABS.onboard_logging.mscRebootFailedCallback = function () {
+    $(".tab-onboard_logging")
+        .toggleClass("msc-supported", false);
+
+    showErrorDialog(i18n.getMessage('operationNotSupported'));
+}

src/tabs/onboard_logging.html

@@ -95,11 +95,10 @@
                             </li>
                         </ul>
                         
-                        <div>
+                        <div class="dataflash-buttons">
                             <a class="regular-button erase-flash" href="#" i18n="dataflashButtonErase"></a>
-                            <span class="require-msc-supported" i18n="dataflashSavingDeprecationNote"></span>
+                            <a class="regular-button require-msc-not-supported save-flash" href="#" i18n="dataflashButtonSaveFile"></a>
-                            <a class="regular-button save-flash" href="#" i18n="dataflashButtonSaveFile"></a>
+                            <a class="regular-button require-msc-supported save-flash" href="#"><span i18n="dataflashButtonSaveFileDeprecated"></span><span class="helpicon cf_tip" i18n_title="dataflashSaveFileDepreciationHint"></span></a>
-                            <span class="require-msc-supported">)</span>
                         </div>
                     </div>